The tool features a user-configurable command line interface that is backed by a computational pipeline, and its job submission graphical user interface is accessible to researchers with limited bioinformatics training.
Data for QC metrics were provided in the submission, but graphical presentation of some metrics would have aided the review.
We have developed a graphical Java-based application (Adamant) to assist with submission of Microarray designs to public repositories.
It is developed in Java and provides a user-friendly graphical user interface for performing the actual data submission, through a series of stages: (1) select all the files needed for the submission; (2) interactively group related files; (3) ensure the minimum level of metadata annotation; and (4) transfer the files via Aspera (http://asperasoft.com/) or FTP.
The database is integrated with analysis tools that include: (i) keyword search, (ii) BLAST, (iii) position-specific iterative BLAST (PSI-BLAST), (iv) FAO/WHO criteria search, (v) graphical representation of allergen information network and (vi) online data submission.
We worked closely with staff at WormBase to develop a graphical display of deletion extents in the genome browser, and to streamline data submission protocols to minimize the time between submission and appearance.
Fig. 3 Graphical user interface (large panel on the left) enabling parameter optimization and job submission to a cluster facility for the reconstruction of full 3D volumes without the need for complex and error-prone command line activity.
For example, while many journals today recommend, or require, the provision of model code during submission (e.g. in SBML), there is no such recommendation to submit also a graphical representation in the Systems Biology Graphical Notations (SBGN) (29), nor to submit the simulation description (in SED-ML).
From 21 submissions, 11 use conditional random fields (CRF), a machine learning method based on undirected graphical models (Bishop, 2006) which leads to competitive results, in our hands 86.33% F1 measure (Klinger et al., 2007b).
There are a number of main innovations of biosoftware_bench: (i) graphical administration; (ii) deployment of command-line software; (iii) use of a secure daemon to handle job submissions with the option to use the Condor job management system; and iv) linking datasets with phylogenetic information.
